|
| Status |
Public on Jun 30, 2017 |
| Title |
H3K27me3-siCSL |
| Sample type |
SRA |
| |
|
| Source name |
H3K27me3 ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: abdomen skin
cell type: primary dermal fibroblasts
genotype/variation: siCSL
passage: 4-6
chip antibody: H3K27m3e (Millipore Cat.No.07-449)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from 5 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibody against H3K27ac, H3K4m3e, H3K27me3 and Polimerase-II. Antibody–chromatin complexes were pulled-down using magnetic beads, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.
NEBNext ChIP-seq Library kit (New England Biolabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5ug Ab/1*10^6 cells
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
Peaks were called using MACS software version 2.1. The input sample H3K27ac-input has been used as control for all the other samples. In order to allow for the identification of the broad peaks from histone markers, the peak model building has been disabled (parameter --nomodel) and a global backgroud signal has been considered (parameter –nolambda).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing the list of peaks identified by MACS
|
| |
|
| Submission date |
May 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Paolo Angelino |
| E-mail(s) |
paolo.angelino@unil.ch, paolo.angelino@sib.swiss
|
| Organization name |
SIB Swiss Institute of Bioinformatics
|
| Department |
BCF
|
| Street address |
Quartier Sorge, Bâtiment Génopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE81404 |
Convergent roles of ATF3 and CSL in chromatin control of CAF activation [HistoneMarkers ChIPseq] |
| GSE81406 |
Convergent roles of ATF3 and CSL in chromatin control of CAF activation |
|
| Relations |
| BioSample |
SAMN04994890 |
| SRA |
SRX1759199 |
